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- PDB-1eoq: ROUS SARCOMA VIRUS CAPSID PROTEIN: C-TERMINAL DOMAIN -

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Basic information

Entry
Database: PDB / ID: 1eoq
TitleROUS SARCOMA VIRUS CAPSID PROTEIN: C-TERMINAL DOMAIN
ComponentsGAG POLYPROTEIN CAPSID PROTEIN P27
KeywordsVIRAL PROTEIN / VIRUS/VIRAL PROTEIN
Function / homology
Function and homology information


host cell nucleoplasm / viral procapsid maturation / host cell nucleolus / Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / viral capsid / structural constituent of virion / nucleic acid binding / aspartic-type endopeptidase activity / host cell plasma membrane / proteolysis ...host cell nucleoplasm / viral procapsid maturation / host cell nucleolus / Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / viral capsid / structural constituent of virion / nucleic acid binding / aspartic-type endopeptidase activity / host cell plasma membrane / proteolysis / zinc ion binding / membrane
Similarity search - Function
Retrovirus capsid C-terminal domain / Retroviral Gag polyprotein, M / Retroviral M domain / Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A / gag protein p24 N-terminal domain / Retropepsin-like catalytic domain / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. ...Retrovirus capsid C-terminal domain / Retroviral Gag polyprotein, M / Retroviral M domain / Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A / gag protein p24 N-terminal domain / Retropepsin-like catalytic domain / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / Retrovirus capsid, C-terminal / Retroviral matrix protein / Retrovirus capsid, N-terminal / zinc finger / Zinc knuckle / Zinc finger, CCHC-type superfamily / Zinc finger, CCHC-type / Zinc finger CCHC-type profile. / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesRous sarcoma virus - Prague C
MethodSOLUTION NMR / torsion angle dynamics, simulated annealing
AuthorsKingston, R.L. / Fitzon-Ostendorp, T. / Eisenmesser, E.Z. / Schatz, G.W. / Vogt, V.M. / Post, C.B. / Rossmann, M.G.
CitationJournal: Structure Fold.Des. / Year: 2000
Title: Structure and self-association of the Rous sarcoma virus capsid protein.
Authors: Kingston, R.L. / Fitzon-Ostendorp, T. / Eisenmesser, E.Z. / Schatz, G.W. / Vogt, V.M. / Post, C.B. / Rossmann, M.G.
History
DepositionMar 23, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 2, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 5, 2019Group: Data collection / Derived calculations / Structure summary
Category: audit_author / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _audit_author.name
Revision 1.4Dec 21, 2022Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GAG POLYPROTEIN CAPSID PROTEIN P27


Theoretical massNumber of molelcules
Total (without water)10,4351
Polymers10,4351
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / -
Representative

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Components

#1: Protein GAG POLYPROTEIN CAPSID PROTEIN P27


Mass: 10435.036 Da / Num. of mol.: 1 / Fragment: C-TERMINAL DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rous sarcoma virus - Prague C / Genus: Alpharetrovirus / Species: Rous sarcoma virus / Strain: PRAGUE C / Plasmid: PET-3XC (NOVAGEN) / Production host: Escherichia coli (E. coli) / References: UniProt: P03322

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1133D 13C-separated NOESY
1223D 15N-separated NOESY
132HNHA
142HNHB
151HNHA
NMR detailsText: The structure was determined using triple-resonance NMR spectroscopy.

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Sample preparation

Details
Solution-IDContentsSolvent system
1U-15N RSV CA(155-249) (used for the 3D_15N-SEPARATED_NOESY, HNHA, HNHB expts) and U-15N/U-13C RSV CA(155-249) (used for the 3D_13C-SEPARATED_NOESY expt) both suspended in the same buffer (50 mM Sodium phosphate pH 4.9 50 mM NaCl 1 mM EDTA 1 mM DTT)90% H20, 10%D20
2U-15N RSV CA(155-249) 50 mM Sodium phosphate pH 4.9 50 mM NaCl 1 mM EDTA 1 mM DTT90% H20, 10%D20
3U-15N,13C RSV CA(155-249) 50 mM Sodium phosphate pH 4.9 50 mM NaCl 1 mM EDTA 1 mM DTT90% H20, 10%D20
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
150 mM NaCl 4.9 ambient 298 K
250 mM NaCl 4.9 ambient 298 K
350 mM NaCl 4.9 ambient 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Varian UNITYPLUS / Manufacturer: Varian / Model: UNITYPLUS / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipe1.6Delaglio, F.processing
ANSIG3.3Kraulis, P.data analysis
CNS1BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE-KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU,READ,RICE,SIMONSON,WARRENrefinement
RefinementMethod: torsion angle dynamics, simulated annealing / Software ordinal: 1
NMR ensembleConformers submitted total number: 1

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